X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=inline;f=treemap.cpp;h=00ae0e664ff5fb7d289893b445be08b5fd20c89a;hb=cdcf99b7760701e6869ca8e4e6e91c8e8c4ae186;hp=6314eb04d04006ba5c57808f6927bddec89d6a00;hpb=b2dca66a02f8f82aa5528e531eace60fbbd2967b;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
index 6314eb0..00ae0e6 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -47,7 +47,7 @@ void TreeMap::readMap() {
 
 int TreeMap::getNumGroups() {
 			
-	return seqsPerGroup.size();	
+	return namesOfGroups.size();	
 		
 }
 /************************************************************/
@@ -72,7 +72,13 @@ string TreeMap::getGroup(string sequenceName) {
 }
 /************************************************************/
 void TreeMap::setIndex(string seq, int index) {
-	treemap[seq].vectorIndex = index;
+	it = treemap.find(seq);
+	if (it != treemap.end()) { //sequence name was in group file
+		treemap[seq].vectorIndex = index;	
+	}else {
+		treemap[seq].vectorIndex = index;
+		treemap[seq].groupname = "not found";
+	}
 }
 /************************************************************/
 int TreeMap::getIndex(string seq) {
@@ -138,3 +144,31 @@ void TreeMap::print(ostream& output){
 }
 
 /************************************************************/
+void TreeMap::makeSim(GroupMap* groupmap) {
+	try {
+		//set names of groups
+		namesOfGroups = groupmap->namesOfGroups;
+		
+		//set names of seqs to names of groups
+		namesOfSeqs = groupmap->namesOfGroups;
+		
+		// make map where key and value are both the group name since that what the tree.shared command wants
+		for (int i = 0; i < namesOfGroups.size(); i++) {
+			treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
+			seqsPerGroup[namesOfGroups[i]] = 1;
+		}
+		
+		numGroups = namesOfGroups.size();
+		
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function make. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the TreeMap class function make. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+/************************************************************/
+